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- PDB-3f40: Crystal structure of NTF2-like protein of unknown function (YP_67... -

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Basic information

Entry
Database: PDB / ID: 3f40
TitleCrystal structure of NTF2-like protein of unknown function (YP_677363.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.27 A resolution
Componentsuncharacterized NTF2-like protein
Keywordsstructural genomics / unknown function / YP_677363.1 / NTF2-like protein of unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein
Function and homology information
Biological speciesCytophaga hutchinsonii ATCC 33406 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.27 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function (YP_677363.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.27 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized NTF2-like protein


Theoretical massNumber of molelcules
Total (without water)13,6421
Polymers13,6421
Non-polymers00
Water2,630146
1
A: uncharacterized NTF2-like protein

A: uncharacterized NTF2-like protein


Theoretical massNumber of molelcules
Total (without water)27,2852
Polymers27,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area1630 Å2
ΔGint-11 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.720, 60.280, 63.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY MEASUREMENTS SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein uncharacterized NTF2-like protein


Mass: 13642.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii ATCC 33406 (bacteria)
Gene: CHU_0736, YP_677363.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q11X43
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.11 %
Description: THE STATISTICS REPORTED IN THE STATEMENTS ABOVE WERE COMPUTED WITH THE FRIEDEL PAIRS KEPT SEPARATE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M MgCl2, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97936,0.91162,0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 10, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979361
20.911621
30.979251
ReflectionResolution: 1.27→27.217 Å / Num. obs: 29394 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.044 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 8.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.27-1.320.5191.912568609897.8
1.32-1.370.4192.310914525897.6
1.37-1.430.3382.811255537497.5
1.43-1.510.233.912511591497.2
1.51-1.60.1435.911110521896.9
1.6-1.720.1077.511665538595.8
1.72-1.90.07210.612444566394.8
1.9-2.170.05214.211680520792.8
2.17-2.730.04716.712015520890.7
2.73-27.2170.04418.912021507287.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.27→27.217 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.829 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.053
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1476 5 %RANDOM
Rwork0.182 ---
obs0.183 29370 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.37 Å2 / Biso mean: 16.062 Å2 / Biso min: 7.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.12 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.27→27.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 0 150 1190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221074
X-RAY DIFFRACTIONr_bond_other_d0.0010.02727
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9481462
X-RAY DIFFRACTIONr_angle_other_deg1.33831779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1845142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6124.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.93815196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.038153
X-RAY DIFFRACTIONr_chiral_restr0.0720.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021255
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02224
X-RAY DIFFRACTIONr_mcbond_it1.4811.5662
X-RAY DIFFRACTIONr_mcbond_other0.8111.5265
X-RAY DIFFRACTIONr_mcangle_it2.28321083
X-RAY DIFFRACTIONr_scbond_it3.5313412
X-RAY DIFFRACTIONr_scangle_it4.7634.5379
X-RAY DIFFRACTIONr_rigid_bond_restr1.89831801
X-RAY DIFFRACTIONr_sphericity_free7.7353152
X-RAY DIFFRACTIONr_sphericity_bonded4.82831767
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 99 -
Rwork0.235 2053 -
all-2152 -
obs--99.63 %

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